Greetings monks, I am *extremely* new to perl, and attempting to use it for a bioinformatics problem. I'm trying to process some bioinformatics data-- I have a large chunk of text which includes information about a group of genes. All of the gene names are in the wrong nomenclature. I want to keep my text file intact, but replace each instance of the incorrect nomenclature with the corresponding correct name. I've put together a hash with the incorrect(current) name for each gene as keys, and the correct(new) name as the values. I figured that I could make my text file into an array, and use some sort of regular expression to find matches to keys in the hash, and replace them with the respective value. I'm not sure how to do this part, and it's a little beyond the scope of the perl manuals I've been using. This is what I have so far:

use warnings;
use strict;

my $infile1 = "InParanoid_Modified.txt";
my $infile2 = "IPArray.txt";
my $outfile = "IPEnsembl.txt";
open (IN1, $infile1) or die $!;
open (IN2, $infile2) or die $!;
open (OUT, ">$outfile") or die $!;
my %Ensembl
while ($infile2 = <IN1>){
    chomp ($infile);
    my @values = split " ", $infile;
    my $ENSG = shift @values;
    foreach my $ENSP(@values){
        $Ensembl{$ENSG} = $ENSP;
}
}
while ($infile1 = <IN1>){
    chomp ($infile1);
    my $IPReplace = translate($infile1);
    print OUT $IPReplace;
}

sub translate {
    my 
close (IN1);
close (IN2);

[download]

any help would be greatly appreciated!

In reply to using a hash as a sort of dictionary by McCaslin

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